So Much for My Favorite 2012 Paper

posted in: Commentary | 8

Republished from Illumination.

Ask any scientist what papers truly intrigued or inspired them.  All of us have a few.

One of my favorites hit Cell Research back in summer of 2012.  In this paper, Zhang et al claimed that dietary microRNAs from rice were somehow ushered through the digestive gauntlet and modulated physiologically relevant changes in LDL, at least in mice.  MicroRNAs are a relatively recent regulatory regimen, a monkey wrench in the central dogma in of molecular biology.  These tiny runs of a 1-2 dozen nucleotides interact with RNA, leading to its degradation. They interact with RNA to change translation and bind to DNA to inspire transcriptional control.  In other words, they place a new layer of complexity into a complex process.

We know that there are 1000+ microRNAs in the human genome and probably just as many in plants.  The work by Zhang was so cool because it said that RNAs from plants could have effects on mammalian physiology.  Mice fed rice experienced changes in gene expression in their livers, apparently imparted by microRNA. It seemed consistent with what we knew about plants and their effects on blood lipoprotein levels.  The paper was really slick– it was exciting to read.

But as I reached the end I could not help but feel the skepticism oozing in.  A little back-of-the-envelope math would reveal that even with liberal estimates there’s no way that a single species of plant microRNA could be present at high enough concentrations to get through postharvest treatment, cooking, digestion, transport, and all of the other hurdles to make the process work as proposed.

The numbers I calculated were ridiculously low, impossible!

But science does have surprises.  I talked about this paper in a journal club with graduate students and remember saying, “When it is repeated or expanded, then we could get excited.”

Of course, the anti-GMO world ignited.  In a discipline founded on what we don’t know will kill us all, the specter of a tiny, rogue RNA was quite frightening.

The Atlantic’s Ari Levaux fans the fire of fear. In his estimation microRNA is clearly poison, and “our bodies are absorbing information….”. Funny, information usually does not get in very fast in my experience.

Levaux was one of many authors that used the news to drive new fears.  After all, the logical anti-GMO syllogism is that GMOs are bad,  GMO food has DNA, DNA makes RNA and RNA can be converted to microRNA.  There. Bingo! Poison!

Of course they completely fail to recognize that every bite of any animal or plant product we consume is already packed with oodles of microRNA.  But that doesn’t matter, that kind isn’t scary.

No new papers came out from Zhang and colleagues describing this paradigm-shifting find.  With time, skepticism grew.

Grow no longer.

Today my bubble was burst, as a solid refutation of the Zhang et al study hit PubMed.  In this work, Dickinson et al. could not detect the same microRNA reported by Zhang et al.

The rice microRNA miR168a was one of the most abundant microRNAs identified in the rice fed to the mice.  They also received several control diets.  Bottom line, there was almost no miR168a identified (well, there was one found in every million miRNAs).  Proper controls were done and the miRNA was detected when spiked in.  Additionally, the authors repeated Zhang’s rice feeding experiment and saw the decrease in LDL, and the changes in LDL did not depend on the availability of miR168a. The observation in Zhang et al that showed differences in the expression of the LDL Receptor Adaptor Protein were also not reproducible in this study.

The authors conclude that the physiology observed from Zhang et al 2012 was due to mice fasting, followed by feeding with rice, causing the LDL spike.

Bummer.  There always is a glimmer of hope that someone will repeat the original study and that there’s some subtle nuance that Zhang did that Dickinson et al neglected.  However, it does not appear that even a partial effect consistent with the original study was observed.  Zhang did offer a rebuttal to the Dickinson work, and it is a little more hand-wavy than hard rebuttal.  More on this later.

Many will dismiss this study because it was done with cooperation from Monsanto.  On the other hand, the other cooperator was miRagen, a company interested in small RNAs for therapies.  They have a vested interest in identifying mechanisms to orally administer miRNA and detect physiological outcomes. If they repeated Zhang et al’s work it would have been a positive finding for their company, as I’m sure they get plenty of criticism for the viability of their potential therapies.

As always, the real science rises to the top.  If the report from Dickinson is the last word, then that’s it.  If Zhang et al are hot on their claims, they will soon publish additional findings and expand on the original report.

I would absolutely love it if the Zhang et al study panned out to be true.  I always love a new crazy layer of science with new avenues to think about and how they can relate to my research.  It is fun to see that things are more complex than we guessed.  That’s good job security. However, today’s paper suggests that I’m probably going to be disappointed.

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Kevin is a public scientist that enjoys illuminating hot-button scientific issues for non-scientists using an evidence-based approach. Kevin is always uncomfortable referring to himself in the third person.